Tue Oct 11 05:17:15 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 05:17:15 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2314 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG8 808 has a net charge of 1.4000 !!! WARNING: ZN8 809 has a net charge of 1.4000 !!! WARNING: ZN8 810 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6909803 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 15.66900 62.79500 ymin,ymax (A): -3.531000 33.38400 zmin,zma (A): 20.14000 71.66100 x,y,z range (A): 47.12600 36.91500 51.52100 scale (grids/A): 0.6909803 object centre (A): 39.23200 14.92650 45.90050 number of atom coordinates read : 2314 total number of charged atoms : 1989 net assigned charge : 9.925008 assigned positive charge : 326.8739 centred at (gu) : 91.41158 89.72685 89.23465 assigned negative charge : -316.9491 centred at (gu) : 91.49503 89.70029 89.14196 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6760 nv = 96 ne = 84 npr = 42584 no. pairs analyzed = 42584 no. exposed pairs = 2553 no. arc points = 17393 no. surface atoms = 873 nbur = 1441 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 3911 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1616 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7618 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8299342E-08 7.6174949E-08 midg,1,midg; midg,igrid,midg 5.0275922E-08 6.2599526E-08 1,midg,midg; igrid,midg,midg 6.4863961E-08 3.6081996E-08 gauss-seidel spectral radius is 0.9890891 estimated iterations to convergence 78 setup time was (sec) 0.5900000 now iterating at: 05:17:16 rms-change max change #iterations 0.1896823 27.23898 at 10iterations 2.2487910E-02 3.422045 at 20iterations 2.6639453E-03 0.4120808 at 30iterations 3.1011945E-04 4.2518616E-02 at 40iterations 3.6882459E-05 5.3653717E-03 at 50iterations finished qdiffx linear iterations at : 05:17:19 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 3.6882459E-05 5.3653717E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 05:17:20 4.042u 0.233s 0:04.91 86.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 05:17:20 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2314 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG8 808 has a net charge of 1.4000 !!! WARNING: ZN8 809 has a net charge of 1.4000 !!! WARNING: ZN8 810 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.072941 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 15.66900 62.79500 ymin,ymax (A): -3.531000 33.38400 zmin,zma (A): 20.14000 71.66100 x,y,z range (A): 47.12600 36.91500 51.52100 scale (grids/A): 2.072941 object centre (A): 39.23200 14.92650 45.90050 number of atom coordinates read : 2314 total number of charged atoms : 1989 net assigned charge : 9.925008 assigned positive charge : 326.8739 centred at (gu) : 94.23451 89.18065 87.70409 assigned negative charge : -316.9491 centred at (gu) : 94.48500 89.10072 87.42616 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 72253 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17393 grid for indexing accessible points = 1.400000 m= 28608 mr = 51341 m= 5325 mr = 21668 m= 453 mr = 3547 m= 7 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 29887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15761 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6909803 object centre at (A) : 39.23200 14.92650 45.90050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9632680E-02 5.1657747E-02 midg,1,midg; midg,igrid,midg 2.7590409E-02 3.4116127E-02 1,midg,midg; igrid,midg,midg 2.6602175E-02 3.2368425E-02 gauss-seidel spectral radius is 0.9987833 estimated iterations to convergence 227 setup time was (sec) 0.9600000 now iterating at: 05:17:21 rms-change max change #iterations 4.513437 182.9253 at 10iterations 2.211117 72.85609 at 20iterations 1.075679 32.58712 at 30iterations 0.5281261 15.54820 at 40iterations 0.2570093 8.654901 at 50iterations 0.1256437 3.616862 at 60iterations 6.1686404E-02 2.050159 at 70iterations 3.0050864E-02 0.9492073 at 80iterations 1.4776260E-02 0.4665718 at 90iterations 7.2267535E-03 0.2240767 at 100iterations 3.5341198E-03 0.1035042 at 110iterations 1.7254819E-03 5.5324554E-02 at 120iterations finished qdiffx linear iterations at : 05:17:29 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 1.7254819E-03 5.5324554E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 05:17:30 9.366u 0.292s 0:09.95 96.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 05:17:30 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2314 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG8 808 has a net charge of 1.4000 !!! WARNING: ZN8 809 has a net charge of 1.4000 !!! WARNING: ZN8 810 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.109411 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 15.66900 62.79500 ymin,ymax (A): -3.531000 33.38400 zmin,zma (A): 20.14000 71.66100 x,y,z range (A): 47.12600 36.91500 51.52100 scale (grids/A): 3.109411 object centre (A): 39.23200 14.92650 45.90050 number of atom coordinates read : 2314 total number of charged atoms : 1989 net assigned charge : 9.925008 assigned positive charge : 326.8739 centred at (gu) : 96.35188 88.77108 86.55612 assigned negative charge : -316.9491 centred at (gu) : 96.72758 88.65104 86.13928 start vw surface at 0.1600000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 166463 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17393 grid for indexing accessible points = 1.400000 m= 89738 mr = 123412 m= 35571 mr = 74737 m= 10158 mr = 29165 m= 1956 mr = 7881 m= 198 mr = 1429 m= 3 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.130000 number of dielectric boundary points 67346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 15912 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.072941 object centre at (A) : 39.23200 14.92650 45.90050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4463683 0.3764084 midg,1,midg; midg,igrid,midg 0.2406241 0.3068287 1,midg,midg; igrid,midg,midg 0.2138696 0.5325714 gauss-seidel spectral radius is 0.9992849 estimated iterations to convergence 295 setup time was (sec) 2.450000 now iterating at: 05:17:33 rms-change max change #iterations 10.13734 406.0692 at 10iterations 5.954686 135.8691 at 20iterations 3.498008 69.45157 at 30iterations 2.051636 39.60482 at 40iterations 1.197156 23.00974 at 50iterations 0.7016098 14.78263 at 60iterations 0.4091109 9.278999 at 70iterations 0.2390227 4.473346 at 80iterations 0.1394516 2.543383 at 90iterations 8.1187151E-02 1.412045 at 100iterations 4.7339670E-02 0.9410629 at 110iterations 2.7546423E-02 0.4958305 at 120iterations 1.6038442E-02 0.3186836 at 130iterations 9.3542570E-03 0.1673095 at 140iterations 5.4734233E-03 9.2216492E-02 at 150iterations 3.2050391E-03 5.8013916E-02 at 160iterations 1.8840791E-03 3.2606125E-02 at 170iterations 1.1220375E-03 2.0256042E-02 at 180iterations finished qdiffx linear iterations at : 05:17:46 total time elapsed so far: 15.95000 # loops : 180 mean,max change (kT/e) : 1.1220375E-03 2.0256042E-02 energy calculations done at 15.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.13000 DelPhi exited at 05:17:47 16.135u 0.303s 0:16.82 97.6% 0+0k 0+0io 0pf+0w